If you have not packed a bike into a box before, assume it will take an hour more than you would normally estimate. You do not want to be rushed.
The day before you leave, make sure your pedals are loose enough you can get them off. Some bike shops put them on really tight.
Figure out what you want to take on the train with you, that includes food and beverages, reading materials, etc. Amtrak carry on policy is MUCH better than airlines. If it is raining when you arrive, you will want rain gear handy. The trains I have been on had 110v outlets, you can plug in a phone or tablet if you want to.
For checked stuff which includes the bike box, Amtrak is pretty firm on weight. I carry a small electronic luggage scale to make sure I am below 50 pounds on my bags, then excess weight if any (dense stuff like tools and spares) goes into a carry on to keep the checked bag below 50 pounds.
I would keep all the tools. How are you going to make sure the pedals get there? Plastic bag for pedals to keep grease off your other stuff?
Maybe add some disposable gloves. I often ask the dental assistant if I can have a few pair for on the road bike repairs, they are always happy to give me a few pair. Harbor Freight also sells nitrile disposable gloves for cheap, boxes of 100.
Some Amtrak stations provide tape, but you are better off to bring it just in case.
My bikes are larger frame sizes, I usually have to remove handlebars to get them into the box, but if your bike is a smaller size frame, the Amtrak box should work fine. That simplifies things a bit.
I usually put two panniers, a water bottle in each cage, and of course the bike, in the Amtrak box, but nothing else.
A very lightweight duffle (mesh ones work pretty good) for your stuff is better than lugging around a heavier one later. I pack stuff in garbage bags inside of mesh lightweight bags. Three of the four bags on the sidewalk are lightweight mesh bags with our gear. Two of those bags were carry on bags.
Put the bike rear derailleur in a lower gear (chain on an inner bigger sprocket in back) so that the derailleur sticks out less and is less likely to get damaged or out of adjustment against the side of box. Sometimes I really have to wonder how the luggage handlers do what they do to get parts of a bike to start leaking out of the boxes.
No flammable liquids or gases on the train, have a plan on where you buy your stove fuel upon arrival. Some Amtrak staff want you to have all liquids in your carry on so they do not have to worry about any leakage in baggage car. Some people break these rules, but I have no idea if you can get in trouble or not. I found out the hard way that REI was out of the stove fuel I wanted to buy in Portland OR when I arrived, I wished I had broken the rule and carried my own fuel there - that really was inconvenient when I had to go searching for stove fuel later.
If you have to drag the cardboard box on pavement across the street, not a big loss, you are throwing the box away later anyway.